Mirror modifiers and multiple Textures
I also encountered that problem while modeling my aircrafts. There are two possible solutions:

The first option is to duplicate the surface where you will put the
logo then separate it into a different object. After that, move or
scale it just above you main object to remove intersections of
meshes. you can now put the logo (make sure it has a transparent
background) and reverse since it is now an individual object and it
will not affect other textures.

The last option is to apply the Mirror modifier then create a new
material just the same as on the other side but the logo that you
will now input into your image texture is reversed. This will be the
texture that you will put apply in the mirrored side of you
aircraft.